diff --git a/.claude-plugin/marketplace.json b/.claude-plugin/marketplace.json index 322deb2..b4768cc 100644 --- a/.claude-plugin/marketplace.json +++ b/.claude-plugin/marketplace.json @@ -6,7 +6,7 @@ }, "metadata": { "description": "Claude scientific skills from K-Dense Inc", - "version": "2.25.0" + "version": "2.26.0" }, "plugins": [ { @@ -31,6 +31,7 @@ "./scientific-skills/deepchem", "./scientific-skills/deeptools", "./scientific-skills/denario", + "./scientific-skills/depmap", "./scientific-skills/diffdock", "./scientific-skills/esm", "./scientific-skills/etetoolkit", @@ -38,8 +39,10 @@ "./scientific-skills/fluidsim", "./scientific-skills/geniml", "./scientific-skills/geopandas", + "./scientific-skills/geomaster", "./scientific-skills/gget", "./scientific-skills/ginkgo-cloud-lab", + "./scientific-skills/glycoengineering", "./scientific-skills/gtars", "./scientific-skills/histolab", "./scientific-skills/imaging-data-commons", @@ -51,13 +54,17 @@ "./scientific-skills/matplotlib", "./scientific-skills/medchem", "./scientific-skills/modal", + "./scientific-skills/molecular-dynamics", "./scientific-skills/molfeat", "./scientific-skills/neurokit2", + "./scientific-skills/neuropixels-analysis", "./scientific-skills/networkx", "./scientific-skills/paper-2-web", "./scientific-skills/pathml", "./scientific-skills/pennylane", "./scientific-skills/perplexity-search", + "./scientific-skills/parallel-web", + "./scientific-skills/phylogenetics", "./scientific-skills/plotly", "./scientific-skills/polars", "./scientific-skills/pydeseq2", @@ -81,6 +88,7 @@ "./scientific-skills/scikit-bio", "./scientific-skills/scikit-learn", "./scientific-skills/scikit-survival", + "./scientific-skills/scvelo", "./scientific-skills/scvi-tools", "./scientific-skills/seaborn", "./scientific-skills/shap", @@ -88,6 +96,8 @@ "./scientific-skills/stable-baselines3", "./scientific-skills/statsmodels", "./scientific-skills/sympy", + "./scientific-skills/tiledbvcf", + "./scientific-skills/timesfm-forecasting", "./scientific-skills/torch_geometric", "./scientific-skills/torchdrug", "./scientific-skills/transformers", @@ -95,8 +105,10 @@ "./scientific-skills/vaex", "./scientific-skills/zarr-python", "./scientific-skills/alphafold-database", + "./scientific-skills/bindingdb-database", "./scientific-skills/biorxiv-database", "./scientific-skills/brenda-database", + "./scientific-skills/cbioportal-database", "./scientific-skills/chembl-database", "./scientific-skills/clinicaltrials-database", "./scientific-skills/clinpgx-database", @@ -109,10 +121,15 @@ "./scientific-skills/fred-economic-data", "./scientific-skills/gene-database", "./scientific-skills/geo-database", + "./scientific-skills/gnomad-database", + "./scientific-skills/gtex-database", "./scientific-skills/gwas-database", "./scientific-skills/hmdb-database", + "./scientific-skills/interpro-database", + "./scientific-skills/jaspar-database", "./scientific-skills/kegg-database", "./scientific-skills/metabolomics-workbench-database", + "./scientific-skills/monarch-database", "./scientific-skills/openalex-database", "./scientific-skills/opentargets-database", "./scientific-skills/pdb-database", @@ -129,6 +146,9 @@ "./scientific-skills/peer-review", "./scientific-skills/scholar-evaluation", "./scientific-skills/scientific-brainstorming", + "./scientific-skills/consciousness-council", + "./scientific-skills/dhdna-profiler", + "./scientific-skills/what-if-oracle", "./scientific-skills/scientific-critical-thinking", "./scientific-skills/scientific-writing", "./scientific-skills/statistical-analysis", @@ -137,8 +157,11 @@ "./scientific-skills/clinical-decision-support", "./scientific-skills/clinical-reports", "./scientific-skills/generate-image", + "./scientific-skills/bgpt-paper-search", + "./scientific-skills/infographics", "./scientific-skills/latex-posters", "./scientific-skills/market-research-reports", + "./scientific-skills/markdown-mermaid-writing", "./scientific-skills/pptx-posters", "./scientific-skills/research-grants", "./scientific-skills/research-lookup", @@ -168,4 +191,4 @@ ] } ] -} \ No newline at end of file +} diff --git a/README.md b/README.md index b87e803..220c254 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,12 @@ # Claude Scientific Skills [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE.md) -[![Skills](https://img.shields.io/badge/Skills-148-brightgreen.svg)](#whats-included) +[![Skills](https://img.shields.io/badge/Skills-170-brightgreen.svg)](#whats-included) [![Databases](https://img.shields.io/badge/Databases-250%2B-orange.svg)](#whats-included) [![Agent Skills](https://img.shields.io/badge/Standard-Agent_Skills-blueviolet.svg)](https://agentskills.io/) [![Works with](https://img.shields.io/badge/Works_with-Cursor_|_Claude_Code_|_Codex-blue.svg)](#getting-started) -A comprehensive collection of **148+ ready-to-use scientific and research skills** (now including financial/SEC research, U.S. Treasury fiscal data, OFR Hedge Fund Monitor, and Alpha Vantage market data) for any AI agent that supports the open [Agent Skills](https://agentskills.io/) standard, created by [K-Dense](https://k-dense.ai). Works with **Cursor, Claude Code, Codex, and more**. Transform your AI agent into a research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond. +A comprehensive collection of **170+ ready-to-use scientific and research skills** (now including cancer genomics, drug-target binding, molecular dynamics, RNA velocity, geospatial science, time series forecasting, FRED economic data, and more) for any AI agent that supports the open [Agent Skills](https://agentskills.io/) standard, created by [K-Dense](https://k-dense.ai). Works with **Cursor, Claude Code, Codex, and more**. Transform your AI agent into a research assistant capable of executing complex multi-step scientific workflows across biology, chemistry, medicine, and beyond.

@@ -46,12 +46,12 @@ These skills enable your AI agent to seamlessly work with specialized scientific ## ๐Ÿ“ฆ What's Included -This repository provides **148 scientific and research skills** organized into the following categories: +This repository provides **170 scientific and research skills** organized into the following categories: - **250+ Scientific & Financial Databases** - Collectively, these skills provide access to over 250 databases and data sources. Dedicated skills cover PubMed, ChEMBL, UniProt, COSMIC, ClinicalTrials.gov, SEC EDGAR, Alpha Vantage, and more; multi-database packages like BioServices (~40 bioinformatics services + 30+ PSICQUIC interaction databases), BioPython (38 NCBI sub-databases via Entrez), and gget (20+ genomics databases) account for the rest -- **55+ Optimized Python Package Skills** - Explicitly defined skills for RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, pyzotero, BioServices, PennyLane, Qiskit, and others โ€” with curated documentation, examples, and best practices. Note: the agent can write code using *any* Python package, not just these; these skills simply provide stronger, more reliable performance for the packages listed +- **60+ Optimized Python Package Skills** - Explicitly defined skills for RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioPython, pyzotero, BioServices, PennyLane, Qiskit, OpenMM, MDAnalysis, scVelo, TimesFM, and others โ€” with curated documentation, examples, and best practices. Note: the agent can write code using *any* Python package, not just these; these skills simply provide stronger, more reliable performance for the packages listed - **15+ Scientific Integration Skills** - Explicitly defined skills for Benchling, DNAnexus, LatchBio, OMERO, Protocols.io, and more. Again, the agent is not limited to these โ€” any API or platform reachable from Python is fair game; these skills are the optimized, pre-documented paths -- **30+ Analysis & Communication Tools** - Literature review, scientific writing, peer review, document processing, posters, slides, schematics, and more +- **35+ Analysis & Communication Tools** - Literature review, scientific writing, peer review, document processing, posters, slides, schematics, infographics, Mermaid diagrams, and more - **10+ Research & Clinical Tools** - Hypothesis generation, grant writing, clinical decision support, treatment plans, regulatory compliance Each skill includes: @@ -91,9 +91,9 @@ Each skill includes: - **Multi-Step Workflows** - Execute complex pipelines with a single prompt ### ๐ŸŽฏ **Comprehensive Coverage** -- **148 Skills** - Extensive coverage across all major scientific domains +- **170 Skills** - Extensive coverage across all major scientific domains - **250+ Databases** - Collective access to 250+ databases and data sources spanning genomics, chemistry, clinical, financial, and more โ€” through dedicated database skills and multi-database packages like BioServices, BioPython, and gget -- **55+ Optimized Python Package Skills** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioServices, PennyLane, Qiskit, and others (the agent can use any Python package; these are the pre-documented, higher-performing paths) +- **60+ Optimized Python Package Skills** - RDKit, Scanpy, PyTorch Lightning, scikit-learn, BioServices, PennyLane, Qiskit, OpenMM, scVelo, TimesFM, and others (the agent can use any Python package; these are the pre-documented, higher-performing paths) ### ๐Ÿ”ง **Easy Integration** - **Simple Setup** - Copy skills to your skills directory and start working @@ -331,7 +331,7 @@ If so, **[K-Dense Web](https://k-dense.ai)** was built for you. It is the full A | Feature | This Repo | K-Dense Web | |---------|-----------|-------------| -| Scientific Skills | 148 skills | **200+ skills** (exclusive access) | +| Scientific Skills | 170 skills | **200+ skills** (exclusive access) | | Setup | Manual installation | **Zero setup, works instantly** | | Compute | Your machine | **Cloud GPUs and HPC included** | | Workflows | Prompt and code | **End-to-end research pipelines** | @@ -394,31 +394,36 @@ If so, **[K-Dense Web](https://k-dense.ai)** was built for you. It is the full A ## ๐Ÿ“š Available Skills -This repository contains **148 scientific and research skills** organized across multiple domains. Each skill provides comprehensive documentation, code examples, and best practices for working with scientific libraries, databases, and tools. +This repository contains **170 scientific and research skills** organized across multiple domains. Each skill provides comprehensive documentation, code examples, and best practices for working with scientific libraries, databases, and tools. ### Skill Categories > **Note:** The Python package and integration skills listed below are *explicitly defined* skills โ€” curated with documentation, examples, and best practices for stronger, more reliable performance. They are not a ceiling: the agent can install and use *any* Python package or call *any* API, even without a dedicated skill. The skills listed simply make common workflows faster and more dependable. -#### ๐Ÿงฌ **Bioinformatics & Genomics** (16+ skills) +#### ๐Ÿงฌ **Bioinformatics & Genomics** (20+ skills) - Sequence analysis: BioPython, pysam, scikit-bio, BioServices -- Single-cell analysis: Scanpy, AnnData, scvi-tools, Arboreto, Cellxgene Census +- Single-cell analysis: Scanpy, AnnData, scvi-tools, scVelo (RNA velocity), Arboreto, Cellxgene Census - Genomic tools: gget, geniml, gtars, deepTools, FlowIO, Zarr, TileDB-VCF -- Phylogenetics: ETE Toolkit +- Phylogenetics: ETE Toolkit, Phylogenetics (MAFFT, IQ-TREE 2, FastTree) -#### ๐Ÿงช **Cheminformatics & Drug Discovery** (11+ skills) +#### ๐Ÿงช **Cheminformatics & Drug Discovery** (13+ skills) - Molecular manipulation: RDKit, Datamol, Molfeat - Deep learning: DeepChem, TorchDrug - Docking & screening: DiffDock +- Molecular dynamics: OpenMM + MDAnalysis (MD simulation & trajectory analysis) - Cloud quantum chemistry: Rowan (pKa, docking, cofolding) - Drug-likeness: MedChem +- Binding affinities: BindingDB (Ki, Kd, IC50, EC50 for drug-target pairs) - Benchmarks: PyTDC #### ๐Ÿ”ฌ **Proteomics & Mass Spectrometry** (2 skills) - Spectral processing: matchms, pyOpenMS -#### ๐Ÿฅ **Clinical Research & Precision Medicine** (12+ skills) +#### ๐Ÿฅ **Clinical Research & Precision Medicine** (16+ skills) - Clinical databases: ClinicalTrials.gov, ClinVar, ClinPGx, COSMIC, FDA Databases +- Cancer genomics: cBioPortal (somatic mutations, CNAs, expression, survival across 400+ studies), DepMap (cancer dependency scores, drug sensitivity) +- Disease-gene associations: Monarch Initiative (OMIM, ORPHANET, HPO, ClinVar, model organism data) +- Cancer imaging: NCI Imaging Data Commons (radiology & pathology datasets via idc-index) - Healthcare AI: PyHealth, NeuroKit2, Clinical Decision Support - Clinical documentation: Clinical Reports, Treatment Plans - Variant analysis: Ensembl, NCBI Gene @@ -430,10 +435,10 @@ This repository contains **148 scientific and research skills** organized across #### ๐Ÿง  **Neuroscience & Electrophysiology** (1 skill) - Neural recordings: Neuropixels-Analysis (extracellular spikes, silicon probes, spike sorting) -#### ๐Ÿค– **Machine Learning & AI** (15+ skills) +#### ๐Ÿค– **Machine Learning & AI** (16+ skills) - Deep learning: PyTorch Lightning, Transformers, Stable Baselines3, PufferLib - Classical ML: scikit-learn, scikit-survival, SHAP -- Time series: aeon +- Time series: aeon, TimesFM (Google's zero-shot foundation model for univariate forecasting) - Bayesian methods: PyMC - Optimization: PyMOO - Graph ML: Torch Geometric @@ -452,12 +457,14 @@ This repository contains **148 scientific and research skills** organized across - Discrete-event simulation: SimPy - Data processing: Dask, Polars, Vaex -#### ๐Ÿ“Š **Data Analysis & Visualization** (14+ skills) +#### ๐Ÿ“Š **Data Analysis & Visualization** (17+ skills) - Visualization: Matplotlib, Seaborn, Plotly, Scientific Visualization -- Geospatial analysis: GeoPandas +- Geospatial analysis: GeoPandas, GeoMaster (remote sensing, GIS, satellite imagery, spatial ML, 500+ examples) - Network analysis: NetworkX - Symbolic math: SymPy - Document processing: Document Skills (PDF, DOCX, PPTX, XLSX) +- Infographics: Infographics (AI-powered professional infographic creation) +- Diagrams: Markdown & Mermaid Writing (text-based diagrams as default documentation standard) - Data access: Data Commons - Exploratory data analysis: EDA workflows - Statistical analysis: Statistical Analysis workflows @@ -473,28 +480,33 @@ This repository contains **148 scientific and research skills** organized across - Multi-omics: Denario, HypoGeniC - Data management: LaminDB -#### ๐Ÿงฌ **Protein Engineering & Design** (2 skills) +#### ๐Ÿงฌ **Protein Engineering & Design** (3 skills) - Protein language models: ESM +- Glycoengineering: Glycoengineering (N/O-glycosylation prediction, therapeutic antibody optimization) - Cloud laboratory platform: Adaptyv (automated protein testing and validation) -#### ๐Ÿ“š **Scientific Communication** (20+ skills) +#### ๐Ÿ“š **Scientific Communication** (24+ skills) - Literature: OpenAlex, PubMed, bioRxiv, Literature Review -- Web search: Perplexity Search (AI-powered search with real-time information) +- Advanced paper search: BGPT Paper Search (25+ structured fields per paper โ€” methods, results, sample sizes, quality scores โ€” from full text, not just abstracts) +- Web search: Perplexity Search (AI-powered search with real-time information), Parallel Web (synthesized summaries with citations) +- Research notebooks: Open Notebook (self-hosted NotebookLM alternative โ€” PDFs, videos, audio, web pages; 16+ AI providers; multi-speaker podcast generation) - Writing: Scientific Writing, Peer Review - Document processing: XLSX, MarkItDown, Document Skills - Publishing: Paper-2-Web, Venue Templates - Presentations: Scientific Slides, LaTeX Posters, PPTX Posters -- Diagrams: Scientific Schematics +- Diagrams: Scientific Schematics, Markdown & Mermaid Writing +- Infographics: Infographics (10 types, 8 styles, colorblind-safe palettes) - Citations: Citation Management - Illustration: Generate Image (AI image generation with FLUX.2 Pro and Gemini 3 Pro (Nano Banana Pro)) -#### ๐Ÿ”ฌ **Scientific Databases** (28+ dedicated skills โ†’ 250+ databases total) -> These 28+ skills each provide direct, optimized access to a named database. Collectively, however, these skills unlock **250+ databases and data sources** โ€” multi-database packages like BioServices (~40 bioinformatics services + 30+ PSICQUIC interaction databases), BioPython (38 NCBI sub-databases via Entrez), and gget (20+ genomics databases) add far more coverage beyond what's listed here. -- Protein: UniProt, PDB, AlphaFold DB -- Chemical: PubChem, ChEMBL, DrugBank, ZINC, HMDB -- Genomic: Ensembl, NCBI Gene, GEO, ENA, GWAS Catalog +#### ๐Ÿ”ฌ **Scientific Databases** (37+ dedicated skills โ†’ 250+ databases total) +> These 37+ skills each provide direct, optimized access to a named database. Collectively, however, these skills unlock **250+ databases and data sources** โ€” multi-database packages like BioServices (~40 bioinformatics services + 30+ PSICQUIC interaction databases), BioPython (38 NCBI sub-databases via Entrez), and gget (20+ genomics databases) add far more coverage beyond what's listed here. +- Protein: UniProt, PDB, AlphaFold DB, InterPro (protein families, domains, Pfam, PANTHER, SMART + 11 others) +- Chemical: PubChem, ChEMBL, DrugBank, ZINC, HMDB, BindingDB (drug-target binding affinities) +- Genomic: Ensembl, NCBI Gene, GEO, ENA, GWAS Catalog, gnomAD (population allele frequencies, pLI/LOEUF), GTEx (tissue-specific expression, eQTLs), JASPAR (transcription factor binding site profiles) - Literature: bioRxiv (preprints) -- Clinical: ClinVar, COSMIC, ClinicalTrials.gov, ClinPGx, FDA Databases +- Clinical: ClinVar, COSMIC, ClinicalTrials.gov, ClinPGx, FDA Databases, cBioPortal (cancer genomics), DepMap (cancer cell line dependencies), Monarch Initiative (rare disease, HPO, cross-species) +- Imaging: NCI Imaging Data Commons (radiology & pathology datasets) - Pathways: KEGG, Reactome, STRING - Targets: Open Targets - Metabolomics: Metabolomics Workbench @@ -508,9 +520,12 @@ This repository contains **148 scientific and research skills** organized across - Automation: Opentrons - Resource detection: Get Available Resources -#### ๐ŸŽ“ **Research Methodology & Planning** (8+ skills) +#### ๐ŸŽ“ **Research Methodology & Planning** (11+ skills) - Ideation: Scientific Brainstorming, Hypothesis Generation - Critical analysis: Scientific Critical Thinking, Scholar Evaluation +- Scenario analysis: What-If Oracle (multi-branch possibility exploration, risk analysis, strategic options) +- Multi-perspective deliberation: Consciousness Council (diverse expert viewpoints, devil's advocate analysis) +- Cognitive profiling: DHDNA Profiler (extract thinking patterns and cognitive signatures from any text) - Funding: Research Grants - Discovery: Research Lookup - Market analysis: Market Research Reports @@ -518,9 +533,10 @@ This repository contains **148 scientific and research skills** organized across #### โš–๏ธ **Regulatory & Standards** (1 skill) - Medical device standards: ISO 13485 Certification -#### ๐Ÿ’น **Financial & SEC Research** (4 skills) +#### ๐Ÿ’น **Financial & SEC Research** (5 skills) - SEC filings & financial data: edgartools (10-K, 10-Q, 8-K, 13F, Form 4, XBRL, insider trading, institutional holdings) - U.S. federal fiscal data: usfiscaldata (national debt, Daily/Monthly Treasury Statements, Treasury auctions, interest rates, exchange rates, savings bonds) +- Macroeconomic data: FRED (800,000+ economic time series from 100+ sources โ€” GDP, unemployment, inflation, housing, regional data via Federal Reserve Economic Data API) - Hedge fund systemic risk: hedgefundmonitor (OFR Hedge Fund Monitor API โ€” Form PF aggregated stats, CFTC futures positioning, FICC sponsored repo, SCOOS dealer financing) - Global market data: alpha-vantage (real-time & historical stocks, options, forex, crypto, commodities, economic indicators, 50+ technical indicators via Alpha Vantage API)